2) alias domain way:
well, basically the same, sometimes it did show the content from an index.php file, but still looped through error pages it could not find and broke.

In my eyes the whole subdomain system is broken since it does not allow to simply enter URL + folder and work, but that's really a different issue, if somebody can point me in the right direction I'm happy as long as I don't have to set up different webspace for each sudomains ( and that's an awful lot ).

If a subdomain shall have its own folder, then create a new website as described in the manual. The subdomain and aliasdomain functions are made for cms systems that are capable of handling multiple domains in one vhost, they are not made to host subdomains in different folders of a website.